Updated code for petsc version 3.6.3

1. Changing KspSetNullspace with MatSetNullspace.
2. Updated FindPETSc.cmake to the changes made in 3.6.xx
3. Use findpetsc.cmake present in the project directory itself instead of
the one present in home directory.

CMakeLists.txt

@@ -14,9 +14,10 @@ else(IS_CLUSTER)
   set(ITK_DIR ${MY_HOME}/Documents/softwares/ITK-build)
   message("setting up for delorme")
 endif(IS_CLUSTER)
-
+MESSAGE("The directory is: ${CMAKE_SOURCE_DIR}")
 #add cmake modules path to the default one:
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${MY_HOME}/cmakeModules/petsc")
+#set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${MY_HOME}/cmakeModules/petsc")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules")
 
 #Find the external library for Petsc
 find_package(PETSc COMPONENTS CXX REQUIRED)

configFiles/petsc_ops_gamg_detailedSummary

@@ -2,11 +2,13 @@
 # This is also a comment line
 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_precondition self
 -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3
--fieldsplit_0_pc_type gamg
+-fieldsplit_0_pc_type gamg -fieldsplit_0_pc_mg_levels_pc_type jacobi
+#-fieldsplit_0_mg_coarse_pc_type svd -fieldsplit_0_mg_coarse_sub_pc_type ?
 #monitor options
 #-fieldsplit_0_ksp_converged_reason
 #-fieldsplit_0_ksp_max_it 100
 -fieldsplit_1_ksp_converged_reason -ksp_converged_reason
-#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8 -ksp_monitor_true_residual
--fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8
+#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+-fieldsplit_1_ksp_monitor -ksp_monitor
 #-log_summary -ksp_view

configFiles/petsc_ops_hypre_detailedSummary

@@ -7,5 +7,7 @@
 #-fieldsplit_0_ksp_converged_reason
 #-fieldsplit_0_ksp_max_it 100
 -fieldsplit_1_ksp_converged_reason -ksp_converged_reason
-#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8 -ksp_monitor_true_residual
--fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual -log_summary -ksp_view
+#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8
+#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+-fieldsplit_1_ksp_monitor -ksp_monitor
+-log_summary -ksp_view

configFiles/petsc_ops_hypre_notDetailedSummary

@@ -7,5 +7,7 @@
 #-fieldsplit_0_ksp_converged_reason
 #-fieldsplit_0_ksp_max_it 100
 #-fieldsplit_1_ksp_converged_reason -ksp_converged_reason
-#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8 -ksp_monitor_true_residual
-#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual -log_summary -ksp_view
+#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8
+#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+#-log_summary -ksp_view

configFiles/petsc_ops_lu

@@ -0,0 +1,13 @@
+# Comment line starts with '#'
+# This is also a comment line
+-pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_precondition self
+-pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3
+-fieldsplit_0_pc_type lu -fieldsplit_1_ksp_rtol 1.0e-10
+#monitor options
+#-fieldsplit_0_ksp_converged_reason
+#-fieldsplit_0_ksp_max_it 100
+-fieldsplit_1_ksp_converged_reason -ksp_converged_reason
+#-fieldsplit_1_ksp_max_it 3 -ksp_max_it 3 -ksp_rtol 1.0e-8
+#-fieldsplit_1_ksp_monitor_true_residual -ksp_monitor_true_residual
+#-fieldsplit_1_ksp_monitor -ksp_monitor
+#-log_summary -ksp_view

src/PetscAdLemMain.cxx

@@ -113,6 +113,7 @@ int opsParser(UserOptions &ops) {
 	ierr = PetscOptionsGetString(NULL,"-boundary_condition",optionString,PETSC_MAX_PATH_LEN,&optionFlag);CHKERRQ(ierr);
         if(!optionFlag) throw "Must provide a valid boundary condition. e.g. dirichlet_at_skull";
         ops.boundaryCondition = optionString;
+
 	ierr = PetscOptionsGetString(NULL,"--relax_ic_in_csf",optionString,PETSC_MAX_PATH_LEN,&optionFlag);CHKERRQ(ierr);
 	ops.relaxIcInCsf = (bool)optionFlag;
 

src/PetscAdLemTaras3D.cxx

@@ -233,24 +233,24 @@ PetscErrorCode PetscAdLemTaras3D::solveModel(bool operatorChanged)
             ierr = DMKSPSetComputeOperators(mDa,computeMatrixTaras3d,this);CHKERRQ(ierr);
             ierr = DMKSPSetComputeRHS(mDa,computeRHSTaras3d,this);CHKERRQ(ierr);
         }
-        if(mPressureNullspacePresent) {
-            ierr = KSPSetNullSpace(mKsp,mNullSpace);CHKERRQ(ierr);//nullSpace for the main system
-        }
         ierr = KSPSetFromOptions(mKsp);CHKERRQ(ierr);
-        ierr = KSPSetUp(mKsp);CHKERRQ(ierr);                  //register the fieldsplits obtained from options.
-
-        ierr = KSPGetOperators(mKsp,&mA,NULL);CHKERRQ(ierr);
-        ierr = KSPGetPC(mKsp,&mPc);CHKERRQ(ierr);
-
-        PetscBool isNull;
+	ierr = KSPSetUp(mKsp);CHKERRQ(ierr); //register the fieldsplits obtained from options.
+	// ---------- MUST CALL kspsetfromoptions() and kspsetup() before kspgetoperators and matsetnullspace
+	// otherwise I'm getting a runtime error of mat object type not set (for mA!!)
+	ierr = KSPGetOperators(mKsp,&mA,NULL);CHKERRQ(ierr);
         if(mPressureNullspacePresent) {
-            ierr = MatNullSpaceTest(mNullSpace,mA,&isNull);CHKERRQ(ierr);
-            if(!isNull) { //FIXME: Must correct this for skull zero boundary condition!
-                //SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"not a valid system null space \n");
-		PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\n WARNING: not a valid system null space\n");
+            //ierr = KSPSetNullSpace(mKsp,mNullSpace);CHKERRQ(ierr);//nullSpace for the main system
+	    ierr = MatSetNullSpace(mA,mNullSpace);CHKERRQ(ierr);//nullSpace for the main system, updated for petsc3.6
+	    PetscBool isNull;
+	    if(mPressureNullspacePresent) {
+		ierr = MatNullSpaceTest(mNullSpace,mA,&isNull);CHKERRQ(ierr);
+		if(!isNull) { //FIXME: Must correct this for skull zero boundary condition!
+		    //SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"not a valid system null space \n");
+		    PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\n WARNING: not a valid system null space\n");
+		}
 	    }
-
-        }
+	}
+        ierr = KSPGetPC(mKsp,&mPc);CHKERRQ(ierr);
 
         //Setting up of null spaces and near null spaces for fieldsplits depend upon the kinds of options user have used.
         PetscBool optionFlag = PETSC_FALSE;
@@ -288,11 +288,13 @@ PetscErrorCode PetscAdLemTaras3D::solveModel(bool operatorChanged)
                             ierr = MatNullSpaceDestroy(&rigidBodyModes);CHKERRQ(ierr);
                         }
 
-                        //If constant pressure nullspace present, set it to SchurComplement ksp.
+                        //If constant pressure nullspace present, set it to SchurComplement matrix.
                         if(mPressureNullspacePresent) {
-                            ierr = KSPSetNullSpace(subKsp[1],mNullSpaceP);CHKERRQ(ierr);
+			    PetscBool isNull;
                             Mat matSc;
                             ierr = KSPGetOperators(subKsp[1],&matSc,NULL);CHKERRQ(ierr);
+			    //ierr = KSPSetNullSpace(subKsp[1],mNullSpaceP);CHKERRQ(ierr); //no longer used in petsc 3.6
+			    ierr = MatSetNullSpace(matSc,mNullSpaceP);CHKERRQ(ierr); //petsc 3.6 update
                             ierr = MatNullSpaceTest(mNullSpaceP,matSc,&isNull);
                             if(!isNull) {//FIXME: Must correct this for skull zero boundary condition!
                                 //SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"not a valid pressure null space \n");